Isolated DNA encoding enzyme for phage resistance

ABSTRACT

An isolated DNA of a Lactococcus lactis showing a SEQ ID NO:1 encoding a restriction and twp modification enzymes (R/M SEQ ID NO: 2, 3 and 4). The isolated DNA is used to transform sensitive dairy cultures, such as Lactococcus lactis and Streptococcus thermophilus, to provide phage resistance. Escherichia coli can be used to produce endonucleases.

This is a divisional of application Ser. No. 08/424,641 filed on Apr. 19, 1995 which is a continuation-in-part of 08/366,480 filed Dec. 30, 1994, now abandoned.

BACKGROUND OF THE INVENTION

(1) Field of the Invention

The present invention relates to transformed dairy cultures with a natural 7.8-kb plasmid pSRQ700 which was isolated from Lactococcus lactis subsp. cremoris DCH-4, a known strain. pSRQ700 encodes a restriction/modification system named LlaII. When introduced into a phage-sensitive dairy culture, such as L. lactis, pSRQ700 confers strong phage resistance against the three most common lactococcal phage species: 936, c2 and P335 found in dairy product fermentations. The LlaII endonuclease was purified and found to cleave the palindromic sequence 5'/GATC-3'. The low copy plasmid pSRQ700 was mapped and the genetic organization of LlaII localized. Cloning and sequencing of the entire LlaII system allowed the identification of three open reading frames. The three genes (LlaIIA, LlaIIB, and LlaIIC) overlapped and are under one promoter. A terminator was found at the end of LlaIIC. The genes LlaIIA and LlaIIB coded for m⁶ A-methyltransferases and LlaIIC for an endonuclease. The native LlaII R/M system from Lactococcus lactis is also expressed by and conferred strong phage resistance to various industrial S. thermophilus strains. Resistance was observed against phages isolated from yogurt and Mozzarella wheys. This is the first demonstration of increased phage resistance in S. thermophilus.

(2) Description of Related Art

Lactococcus lactis and Streptococcus salivarius subsp. thermophilus cultures are used extensively worldwide in the manufacture of fermented dairy products. The cultures are normally inoculated into pasteurized or heat-treated milk to quickly start and control the fermentation. In this non-sterile milk environment, the added cells come into contact with the wild bacteriophage population that has survived pasteurization. Although natural phage concentration is low, their population increases very rapidly if phage-sensitive cells are present in the starter culture. The consequent lysis of a large number of sensitive cells retards the fermentation process. To cope with this natural phenomenon, the dairy industry has developed a series of solutions including the use of phage resistant Lactococcus lactis strains (Hill, C., FEMS Microbiol. Rev. 12:87-108 (1993)).

Lactococcus lactis

In the last decade, extensive research was conducted on interactions between lactococcal phage and their hosts. Lactococcus lactis was found to possess many plasmids coding for natural defense mechanisms against bacteriophages. Over 40 plasmids with phage defense barriers have been identified. Phage resistance systems are classified into three groups based on their mode of action: blocking of phage adsorption, restriction/modification and abortive infection. Phage-resistant Lactococcus lactis strains have been constructed by introducing these natural plasmids into phage-sensitive strains (Sanders, M. E., et al., Appl. Environ. Microbiol. 40:500-506 (1980)). The conjugative abilities of some of these plasmids was exploited to construct such resistant strains (Harrington, A., et al., Appl. Environ. Microbiol. 57:3405-3409 (1991); Jarvis, A. W., et al., Appl. Environ. Microbiol. 55:1537-1543 (1988); Sanders, M. E., et al., Appl. Environ. Microbiol. 52:1001-1007 (1986); and Ward, A. C., et al., J. Dairy Sci. 75:683-691 (1992)). However, after considerable industrial use of these strains, new phages capable of overcoming the introduced defense mechanism have emerged (Alatossava, T., et al., Appl. Environ. Microbiol. 57:1346-1353 (1991); Hill, C., et al., J. Bacteriol. 173:4363-4370 (1991); and Moineau, S., et al., Appl. Environ. Microbiol. 59:197-202 (1993)). Thus, the search for different natural phage barriers is still an ongoing objective for dairy product starter culture manufacturers.

Over the years several studies have established the heterologous nature of the lactococcal phage population (Jarvis, A. W., et al., Intervirology 32:2-9 (1991)). Based on electron microscopy and DNA hybridization studies, the Lactococcal and Streptococcal Phage Study Group, which is part of the International Committee on Taxonomy of Viruses, reported the existence of 12 different lactococcal phage species. Recently, this number has been reduced to 10 due to the reclassification of the 1483 and T187 species into the P335 species. Strong DNA homology is observed among members of the same species but no homology is found between species (Braun, V., et al., J. Gen. Microbiol. 135:2551-2560 (1989); Jarvis, A. W., et al., Intervirology, 32:2-9 (1991); Moineau, S., et al., Can. J. Microbiol. 38:875-882 (1992); Powell, I. A., et al., Can. J. Microbiol. 35:860-866 (1989); and Prevots, F., et al., Appl. Environ. Microbiol. 56:2180-2185 (1990)). Although many species have been isolated, only three appear to be the most problem for the dairy industry. The species 936 (small isometric head) and c2 (prolate head) have been, by far, the most disturbing lactococcal phage species worldwide. Interestingly, phages from the P335 species (small isometric head) are now being isolated with increasing frequency from North American dairy plants (Moineau, S., et al., Appl. Environ. Microbiol. 59:197-202 (1993)). Two recent surveys revealed that 100% of the 45 lactococcal phages isolated from Canadian cheese plants and U.S. buttermilk plants were classified within one of these three species: 22 phages belonged to the 936 species, 18 to the c2 species and 5 to the P335 species (Moineau, S., et al., J. Dairy Sci. 77:18 suppl. 1 (1994); and Moineau, S., et al., Can. J. Microbiol. 38:875-882 (1992)). Therefore from a practical point of view, industrial Lactococcus lactis strains should at least be resistant to the three most common phage species: 936, c2 and P335. Due to the diversity of lactococcal phages, the need for phage defense mechanisms with broad activity (attacking many species) is becoming more meaningful. Because of the characteristics of phages, restriction/modification (R/M) systems have the potential to fulfill this objective.

The phenomenon of R/M was first reported more than 40 years ago (Luria, S. E., et al., J. Bacteriol. 64:557-569 (1952)) and received a molecular explanation ten (10) years later (Bickle, T. A., et al., Microbiol. Rev. 57:434-450 (1993); and Dussoix, D., et al., J. Mol. Biol. 5:37-49 (1962)). The main biological activity of R/M is believed to be in preventing the entrance of foreign DNA (including phage DNA) into the cell. These gatekeepers are roughly the prokaryotic equivalent of the immune system (Wilson, G. G., Nucleic Acids Res. 19:2539-2566 (1991)). There are currently more than 2400 known restriction enzymes and over 100 have been cloned and sequenced (Raschke, E., GATA 10:49-60 (1993); and Roberts, R. J., et al., Nucleic Acid Res. 21:3125-3137 (1993)). There are several kinds of R/M systems and they appear to have equivalent biological activities but achieved in different ways. At least four types of R/M systems have been identified: I, II, IIs, and IIII (Bickle, T. A., et al., Microbiol. Rev. 57:434-450 (1993); Wilson, G. G., Nucleic Acids Res. 19:2539-2566 (1991); and Wilson, G. G., et al., Annu. Rev. Genet. 25:585-627 (1991)). Of these, type II is the simplest and the most common. Illustrative patents are European Patent Application 0 316 677, European Patent Application 0 452 224, U.S. Pat. Nos. 4,530,904 to Hershberger, et al, 4,883,756 to Klaenhammer et al, 4,931,396 to Klaenhammer et al and 5,019,506 to Daly et al.

Many R/M systems have been characterized at the protein level. Restriction enzymes are very dissimilar, suggesting an independent evolution and not from a common ancestor (Bickle, T. A., et al., Microbiol. Rev. 57:434-450 (1993); Wilson, G. G., Nucleic Acids Res. 19:2539-2566 (1991); and Wilson, G. G., et al., Annu. Rev. Genet. 25:585-627 (1991)). In contrast, extensive similarities occur among the methyltransferases (Bickle, T. A., et al., Microbiol. Rev. 57:434-450 (1993); Klimasauskas, S., et al., Nucleic Acids Res. 17:9823-9832 (1989); Lauster, R., J. Mol. Biol. 206:313-321 (1989); McClelland, M., et al., Nucleic Acids Res. 20:2145-2157 (1992); Wilson, G. G., Nucleic Acids Res. 19:2539-2566 (1991); and Wilson, G. G., et al., Annu. Rev. Genet. 25:585-627 (1991)). They can be grouped into three classes corresponding to the modification types: m⁴ C, m⁵ C and m⁶ A (Wilson, G. G., Nucleic Acids Res. 19:2539-2566 (1991); and Wilson, G. G., et al., Annu. Rev. Genet. 25:585-627 (1991)). m⁴ C and m⁶ A can be further divided in two (α and β) and three (α, β, and γ) subclasses respectively, based on their amino acid sequences (Klimasauskas, S., et al., Nucleic Acids Res. 17:9823-9832 (1989); and Lauster, R., J. Mol. Biol. 206:313-321 (1989)).

A number of plasmids encoding for R/M have been identified in Lactococcus (Hill, C., FEMS Microbiol. Rev. 12:87-108 (1993)). Surprisingly, only a handful have been partially characterized. The LlaI R/M system encoded on the conjugative plasmid pTR2030, isolated from Lactococcus lactis subsp. lactis ME2, was the first analyzed at the sequence level (Hill, C., et al., J. Bacteriol. 173:4363-4370 (1991)). The methylase gene of pTR2030 system has been sequenced and the deduced protein was found to share similarities with the type-IIs methyltransferase (m⁶ A), M. FokI (Hill, C. L., et al., J. Bacteriol. 173:4363-4370 (1991)). The endonuclease genes have also been sequenced and four open reading frames were identified (O'Sullivan, D. J., et al., FEMS Microbiol. Rev. 12:P100 (1993)). Recent data have provided evidence for a new class of multisubunit endonucleases (O'Sullivan, D. J., et al., FEMS Microbiol. Rev. 12:P100 (1993)). The restriction complex, however, has yet to be purified and its recognition sequence is unknown.

ScrFI was the first classical type II restriction enzyme isolated from Lactococcus lactis and is the only one commercially available (Fitzgerald, G. F., et al., Nucleic Acid Research. 10:8171-8179 (1982)). ScrFI recognizes the sequence 5'-CCNGG-3' where N is any of the nucleotide. Two methylase genes from the Lactococcus lactis subsp. lactis UC503 chromosome have been cloned and sequenced (Davis, R., et al., Appl. Environ. Microbiol. 59:777-785 (1993); and Twomey, D. P., et al., Gene 136:205-209 (1993)). They both coded for a m⁵ C MTase. The endonuclease gene has yet to be identified. Mayo et al (Mayo, B., et al., FEMS Microbiol. Lett. 79:195-198 (1991) isolated a type II endonuclease (also named LlaI) from L. lactis subsp. lactis NCDO497 which recognized the sequence 5'-CCWGG-3 (W is A or T) but the R/M genes have not been cloned.

Recently Nyengaard, N., et al, Gene 136, 371-372 (1993) described LlaI and LlaBI, which are type II restriction endonucleases from Lactococcus lactis subsp. cremoris W9 and W56. These endonucleases recognize DNA sequences 5'/GATC-3 and 5'-C/TRYAG3', respectively. The plasmids from these strains were transformed into a plasmid free and endonuclease negative Lactococcus lactis subsp. lactis by electroporation to produce a transformed strain which resisted phage attack. The DNA was not isolated and sequenced and the natural plasmid was used for the transformation. Further, the authors did not indicate if the plasmids encoded methyl transferase. Strains W9 and W56 were not tested.

Streptococcus thermophilus

Similar information on phage and phage resistance is still very limited for Streptococcus thermophilus despite sustained phage infections in the yogurt and Mozzarella cheese industry (Mercenier et al, Genetic engineering of lactobacilli, leuconostocs and Streptococcus thermophilus, In M. J. Gasson and W. M. DeVos (ed.), Genetics and biotechnology of lactic acid bacteria. Blackie Acad. Prof. Glaskow, UK p. 253-293 (1994)). Fortunately, S. thermophilus phages are much more closely related to each other than the L. lactis phages. It appears that there is only one S. thermophilus phage species (Mercenier et al Genetic engineering of lactobacilli, leuconostocs and Streptococcus thermophilus, In M. J. Gasson and W. M. DeVos (ed.), Genetics and biotechnology of lactic acid bacteria. Blackie Acad. Prof. Glaskow, UK p. 253-293 (1994)). Only very few phage defense mechanisms have been reported for S. thermophilus. Four chromosomally-encoded type II R/M systems have been identified in S. thermophilus. Solaiman and Somkuti (Solaiman, D. K. Y., et al., FEMS Microbiol. Lett. 67:261-266 (1990); and Solaiman, D. K. Y., et al., FEMS Microbiol. Lett. 80:75-80 (1991)) have isolated the endonuclease Sth134I and Sth117I which are isoschizomers of HpaII and EcoRII, respectively. Benbadis et al (Benbadis, L., et al., Appl. Environ. Microbiol. 57:3677-3678 (1991)) and Guimont et al (Guimont, C., et al., Appl. Microbiol. Biotechnol. 39:216-220 (1993)) have isolated the endonucleases sslI and Sth455I, respectively. Both are also isoschizomers of EcoRII. In addition, S. thermophilus might possess abortive-like phage defense mechanisms (Larbi et al. J. Dairy Res. 59:349-357 (1992)), although definitive proof has yet to be demonstrated. None of the R/M systems so far identified in S. thermophilus have been cloned, sequenced, or used in commercial strains for improvement of phage resistance. There is believed to be no report on improvement of phage resistance of S. thermophilus strains.

OBJECTS

It is therefore an object of the present invention to provide an isolated DNA encoding only restriction and modification enzymes to impart phage resistance. Further, it is an object of the present invention to provide transformation vectors and transformed bacteria incorporating the DNA which are particularly useful in the dairy industry. These and other objects will become increasingly apparent by reference to the following description and the drawings.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 is an electrophoresis gel showing a plasmid analysis of Lactococcus lactis strains wherein Lane 1 is supercoiled DNA ladder (GIBCO/BRL); Lane 2 is Lactococcus lactis DCH-4; Lane 3 is Lactococcus lactis SMQ-17 (pSA3 and pSRQ700); Lane 4 is Lactococcus lactis SMQ-16 (pSA3).

FIG. 2 is an endonuclease restriction map of lactococcal plasmid pSRQ700. Site positions are indicated in kb.

FIG. 3 is a map showing cloning of LlaII from pSRQ700 into pSA3. Clones were electroporated into LM0230. Transformants were tested for phage resistance against .O slashed.p2.

FIGS. 4A to 4C are a nucleotide sequence of the 3-kb Nrul-EcoRV fragment from pSRQ700. The deduced amino acid sequence of the 3 ORFs is presented. The putatives promoter, terminator and ribosome binding site are underlined. The first codon of each ORF is in bold. The amino acids are in single letter code.

FIGS. 5A to 5C are charts showing a comparison of the amino acids between A) M.M. LlaIIA (SEQ ID NO. 2), M. DpnII (SEQ ID NO. 5), M.MboA (SEQ ID NO. 6) and E. coli Dam (SEQ ID NO. 7) methylases; B) M.LlaIIB (SEQ ID NO. 3), DpnA (SEQ ID NO. 8), M.MboC (SEQ ID NO. 9) and M.HinfI (SEQ ID NO. 10); C) R.LlaII (SEQ ID NO. 4), R.DpnII (SEQ ID NO. 11) and R.MboI (SEQ ID NO. 12). The asterisk (*) indicates conserved amino acids. Bars show gaps in the aligned sequences.

FIG. 6 is an electrophoresis gel showing restriction patterns of .O slashed.Q1, .O slashed.Q3 and .O slashed.Q5. Lane 1 and 5, 1-kb ladder (Bethesda Research Laboratories); Lane 2, .O slashed.Q1 DNA cut with EcoRV, Lane 3, .O slashed.Q2 cut with EcoRV; Lane 4, .O slashed.Q5 cut with EcoRV; Lane 6, .O slashed.Q1 cut with Mbol; Lane 7, .O slashed.Q7 cut with Mbol; Lane 8, .O slashed.Q5 cut with Mbol.

FIG. 7 is a schematic flow sheet showing the construction of the plasmids used in this study.

DESCRIPTION OF PREFERRED EMBODIMENTS

The present invention relates to an isolated DNA encoding only an enzyme which is sufficiently duplicative of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC and mixtures thereof to restrict or modify a phage. Further the present invention relates to an isolated DNA having a nucleotide sequence essentially as set forth in SEQ ID NO. 1 selected from the group consisting of ORF1 (positions 97 to 948), ORF2 (positions 941 to 1747) and ORF3 (positions 1740 to 2651) and combinations thereof.

The present invention also relates to a recombinant plasmid containing DNA encoding an enzyme sufficiently duplicative of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC and mixtures thereof to restrict or modify a phage.

Further the present invention relates to a bacterium harboring a recombinant plasmid containing DNA encoding for an enzyme sufficiently duplicative of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC and mixtures thereof to restrict or modify a phage.

Further still, the present invention relates to a recombinantly produced purified protein which is an enzyme containing a sequence of amino acids sufficiently duplicative of that set forth in a member selected from the group consisting of ORF 1, ORF 2 and ORF 3 and combinations thereof in SEQ ID NO. 2, 3 or 4 such that restriction or modification of a phage can be performed with the enzyme, wherein the protein has been produced from isolated DNA of the SEQ ID NO:1. The protein can be used for assays as described hereinafter.

Further, the present invention relates to a method of imparting phage resistance to a bacterium which is sensitive to the phage which comprises incorporating recombinant DNA encoding an enzyme sufficiently duplicative of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC and mixtures thereof into the bacterium to impart the phage resistance, wherein the DNA encoding the member is contained in strain Lactococcus lactis SMQ-17 deposited with the Agricultural Research Service Culture Collection, 1815 N. University St., Peoria, Ill. 61604, as NRRL-B-21337. Preferably the bacterium is a dairy culture. In particular, the present invention relates to a bacterium, preferably isolated and purified, selected from the group consisting of Streptococcus salivarius subsp. thermophilus and Lactococcus lactis naturally lacking in phage resistance which bacterium contains recombinant DNA encoding for an enzyme sufficiently duplicate of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC and having a sequence of the DNA for the member is essentially as set forth in SEQ ID NO:1 to impart phage resistance.

Finally, the present invention relates to a method for fermenting a dairy product, the improvement which comprises using a dairy culture selected from the group consisting of Lactococcus lactis and Streptococcus salivarius subsp. thermophilus incorporating recombinant DNA encoding for an enzyme sufficiently duplicative of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC to impart phage resistance, wherein the DNA for the member is contained in strain Lactococcus lactis SMQ-17 deposited as NRRL-B-21337. The DNA is generally transformed into the dairy culture.

The DNA of SEQ ID NO:1 and FIGS. 4A to 4C (Appendix I) is contained in Lactococcus lactis SMQ-17 deposited under the Budapest Treaty on Sep. 29, 1994 as NRRL-B-21337. The strain is available upon request by name and deposit number. The isolated DNA is obtained by means of EcoRV or Nru1-TcoRV digestion of pSRQ700 as described hereinafter.

The art of DNA isolation and cloning is well known to those skilled in the art. Further, the terminology of this art is well developed, see for instance EP 0316677 A2. As used herein, the term "transformed" means to transfer DNA from one bacterium to another in related bacterium. The term "recombinant" as used herein means DNA in a form not existing in nature. In general the recombinant DNA contains DNA encoding only one or more of the sequence of amino acids for LlaIIA, LlaIIB and LlaIIC as set forth in SEQ ID NO:1. The recombinant enzymes encoded are like the natural enzymes except that the physical configurations are different and they are thus different. They retain the ability to restrict or modify (methylate) the phage DNA.

Various shuttle vectors can be used. pSA3 from Dao, M., et al., Applied Environ. Microb. 49:115-119 (1985) was used.

The recombinant bacterium can be for instance Escherichia coli, a Lactococcus sp. or a Streptococcus sp. used in dairy fermentations. The E. coli are used to produce the enzymes of SEQ ID NO:2, 3 and/or 4 which can be used to produce a DNA or RNA probe in a known manner or can be used to produce antibodies to the enzymes in a well known manner for use in assays for the enzymes. Purification of the enzymes is achieved using affinity chromatography and/or molecular filtration.

The DNA of SEQ ID NO:1 can have modifications in sequence and still be homologous and still encode enzymes which have the necessary phage resistance properties. Generally within 75-100% homology is sufficient.

The preferred use of the transformed cultures containing the recombinant DNA of SEQ ID NO:1 is in dairy product fermentations. Such fermentations are well known to those skilled in the art. The preferred strains are transformed Lactococcus lactis and Streptococcus salivarius sp. thermophilus which are used in the dairy product fermentations.

EXAMPLE 1

Bacterial strains, plasmids, and media

The strains and plasmids and enzymes used in this invention are listed in Tables 1 and 2.

                                      TABLE 1     __________________________________________________________________________     Bacterial strains, plasmids and bacteriophages.     Bacteria, plasmids,     and phages  Relevant characteristics                                  Source     __________________________________________________________________________     L. lactis subsp. cremoris     DCH-4       Industrial strain, multiple                                  Invention                 plasmids, Lac.sup.+     UL8         Industrial strain, host for P335                                  Moineau, S., et al.,                 phages, Lac.sup.+                                  Can J. Microbiol. 38:                                  875-882 (1992)     SMQ-87      UL8 (pSRQ701), Lac.sup.+, Em.sup.r                                  Invention     L. lactis subsp. lactis     LM0230      Plasmid free, host for 936                                  McKay, L. L., et al,                 and c2 phages, Lac.sup.-                                  Appl. Environ. Microbiol.                                  23:1090-1096 (1972)     SMQ-16      LM0230 (pSA3), Lac.sup.-, Em.sup.r.                                  Invention     SMQ-17      LM0230 (pSA3, pSRQ700), Lac.sup.-, Em.sup.r                                  Invention     SMQ-39      LM0230 (PSRQ701), Lac.sup.-, Em.sup.r                                  Invention     SMQ-40      LM0230 (pSRQ702), Lac.sup.-, Em.sup.r.sup.c                                  Invention     SMQ-50      LM0230 (pSRQ703), Lac.sup.-, Em.sup.r                                  Invention     SMQ-117     LM0230 (pSRQ704), Lac.sup.-, Em.sup.r                                  Invention     SMQ-140     LM0230 (pSRQ706), Lac.sup.-, Em.sup.r                                  Invention     E. coli     DH5α  Transformation host                                  GIBCO/BRL                                  (Grand Island, NY)     DMQ-149     DH5α(pSRQ708), Apr                                  Invention     Pages     .O slashed.p2                 Small isometric headed, 936                                  L. L. McKay                 species, 30.5 kb     .O slashed.sk1                 Small isometric headed, 936                                  L. L. McKay                 species, 28.1 kb     .O slashed.jj50                 Small isometric headed, 936                                  J. Josephsen, et al.,                 species, 30.5 kb FEMS Microbiol. Lett.                                  59:161-166 (1989)     .O slashed.c2                 Prolate headed, c2 species,                                  Sanders, M.E., et al.,                 20.7 kb          Appl. Environ. Microbiol.                                  40:500-596 (1980)     .O slashed.m13                 Prolate headed, c2 species,                                  W. E. Sandine                 20.2 kb     .O slashed.eb1                 Prolate headed, c2 species,                                  L. L. McKay                 19.6 kb     .O slashed.ul36                 Small isometric headed, P335                                  Moineau, S., .et al.,                 species, 28.8 kb Can J. Microbiol. 38:                                  875-882 (1992)     .O slashed.Q30                 Small isometric headed, P335                                  Moineau, S., et al.,                 species, 37.0 kb J. Dairy Sci.                                  77:18 Suppl. 1 (1994)     .O slashed.Q33                 Small isometric headed, P335                                  Moineau, S., et al.,                 species, 29.6 kb J. Dairy. Sci.                                  77:18 Suppl. 1 (1994)     __________________________________________________________________________      L. L. McKay, University of Minnesota; W. E. Sandine, Oregon State      University;. Lac, lactosefermenting ability; Ap.sup.4, ampicillin      resistance; Cm.sup.r, chloramphenicol resistance; Em.sup.r, erythromycin      resistance.

                                      TABLE 2     __________________________________________________________________________     Plasmids used in this study     Plasmid Relevant characteristics               Source     __________________________________________________________________________     pSA3    Shuttle vector, Cm, Tc, Em, 10.2 kb.   Dao, M.L., et al., Appl.                                                    Env.Microb.                                                    49:115-119(1985)     pBS KS(+)             Cloning vector for sequencing, Ap, 2.9 kb.                                                    Stratagene     pSRQ700 Resident plasmid of DCH-4, R.sup.+ /M.sup.+, 7.8                                                    This study     pSPQ701 7.0-kb EcoRI fragment from pSRQ700 cloned into pSA3, R.sup.+             /M.sup.+, Cm.sup.S, Tc.sup.r, Em.sup.r.                                                    This study     pSRQ702 5.3-kb Ncol-EcoRI fragment from pSRQ700 cloned into pSA3,             R/M.sup.+, Cm.sup.S, Tc.sup.r, Em.sup.r.                                                    This study     pSRQ703 6 6-kb Ncol fragment from pSRQ700 cloned into pSA3, R.sup.+             /M.sup.+, Cm.sup.S, Tc.sup.r, Em.sup.r.                                                    This study     pSRQ704 7.8-kb EcoRV fragment from pSRQ700 cloned into pSA3, R.sup.+             /M.sup.+, Cm.sup.r, Tc.sup.S, Em.sup.r.                                                    This study     pSRQ706 3.0-kb Nrul-EcORV fragment from pSRQ700 cloned info pSA3 R.sup.+             /M.sup.+, Cm.sup.r, Tc.sup.S, Em.sup.r.                                                    This study     pSRQ708 3.0-kb Nrul-ECORV fragment from pSRQ700 cloned into pBS, R.sup.+             /M.sup.+, Ap.sup.r.                    This study     __________________________________________________________________________      AP.sup.r, ampicillin resistance, Cm.sup.r, chloramphenicol resistance;      Cm.sup.S, sensitive to chloramphenicol; Em.sup.r, erythromycin resistance      Tc.sup.r, tetracycline resistance; Tc.sup.S, tetracycline resistance;      R.sup.+ /M.sup.+, active restriction/active modification enzymes.

Escherichia coli was grown at 37° C. in Luria-Bertani (Sambrooke, J., et al., Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989)). Lactococcus lactis strains were grown at 30° C. in M17 (Terzaghi, B. E., et al., Appl. Microbiol. 29:807-813 (1975)) supplemented with 0.5% glucose (GM17) or 0.5% lactose (LM17). When appropriate, antibiotics were added as follows: for E. coli, 50 μg/ml of ampicillin (Ap), 10 μg/ml of tetracycline (Tc), and 20 μg/ml of chloramphenicol (Cm); for L. lactis, 5 μg/ml of erythromycin (Em).

Bacteriophage propagation and assays

Bacteriophages used in this invention are listed in Table 1. Bacteriophages were propagated and titrated by the method of Jarvis (Jarvis, A. W., Appl. Environ. Microbiol. 36:785-789 (1978)). Efficiency of plaquing (EOP) assays were performed as described by Sanders and Klaenhammer (Sanders, M. E., et al., Appl. Environ. Microbiol. 40:500-506 (1980)). Bacteriophages c2, p2, sk1 and jj50 were supplied by T. R. Klaenhammer (North Carolina State University).

DNA Isolation and manipulation

Plasmid DNA from E. coil was isolated as described previously (Moineau, S., et al., Appl. Environ. Microbiol. 60:1832-1841 (1994)). Large quantities of E. coli plasmid DNA was isolated by using plasmid MIDI or MAXI kit (Qiagen Inc., Chatsworth, Calif.). Plasmid DNA from L. lactis was isolated as described by O'Sullivan and Klaenhammer (O'Sullivan, D. J., et al., Appl. Environ. Microbiol. 59:2730-2733 (1993)). Large quantity of lactococcal plasmid DNA was obtained using the Leblanc and Lee procedure (Leblanc, D. J., et al., J. Bacteriol. 140:1112-1115 (1979)) as modified by Gonzalez and Kunka (Gonzalez, C. F., et al., Appl. Environ. Microbiol. 46:81-89 (1983)). Restriction endonucleases (Gibco/BRL, Grand Island, N.Y.) and T4 DNA ligase (Boehringer Manheim, Indianapolis, Ind.) were used according to manufacturer's instructions. When needed, DNA fragments were obtained from low-melting agarose using a QIAEX gel extraction kit (Qiagen, Inc., Chatsworth, Calif.).

Electroporation

E. col was grown, electroporated, incubated, and plated as described previously (Moineau, S., et al., Appl. Environ. Microbiol. 60:1832-1841 (1994)). L. lactis was grown in GM17 supplemented with 0.5M sucrose (SGM17) and 1% glycine and electroporated as described by Holo and Nes (Holo, H., et al., Appl. Environ. Microbiol. 55:3119-3123 (1989)). The Gene Pulser apparatus (Bio-Rad Laboratories, Richmond, Calif.) was set at 25 μF and 2.45 kV, and the Pulse Controller was set at 200 Ω. Plasmid DNA was mixed with 40 μl of cells in a chilled cuvette (0.2 cm). After electroporation, L. lactis cells were resuspended in SGM17, incubated for 2 h at 30° C., plated on GM17 supplemented with erythromycin (5 μg/ml) and incubated for 2 days at 30° C.

Sequencing

The entire LlaII system (3 kb NruI-EcoRV fragment from pSRQ700) was cloned into E. col pBluescript. The resulting clone was named pSRQ708. Nested deletions were made in both orientations from pSRQ708 using the ERASE-A-BASE kit (Promega, Madison, Wis.). For the first set of deletions, the endonucleases SstI was used for protection and XbaI to start the deletion. The restriction pairs KpnI-DraII were used to obtain the nested deletions in the other orientation. Plasmid DNA was extracted from the nested clones with QIAGEN and directly used for sequencing. The sequencing reactions were performed using the DYEDEOXY TERMINATOR TAQ sequencing kit for use on the 373A automated DNA sequencing system (Applied Biosystems, Foster City, Calif.). The T7 and T3 primers were used for annealing.

Restriction enzyme purification

L. lactis SMQ-17 was grown in 2 L, concentrated by centrifugation (10,000 rpm, 15 min.) and washed twice in saline. The cells were then resuspended in 30 ml of PME buffer (10 mM NaH₂ PO₄ pH 7.4, 0.1 mM EDTA and 10 mM β-mercaptoethanol). Cells were lysed by 15 bursts (30 seconds each followed by one minute rest) with glass beads and a bead beater (BIOSPEC, Bartlesville, Okla.). After centrifugation to remove cell debris and glass beads, the supernatant was used for ion exchange chromatography. Successive chromatographies were performed on phosphocellulose (Whatman P11, Maidstone, England) and dimethylaminoethyl cellulose (Whatman DE5, Maidstone, England) using a salt gradient in PME buffer. Restriction endonuclease activity was found in the fractions around 0.5 M NaCl. Lactococcal phage ul36 DNA was used as substrate and the digestions were performed at 37° C. for 2-4 h using the buffer system #2 from GIBCO/BRL (50 mM Tris-HCl pH 8.0, 10 mM MgCl₂, 50 mM NaCl). DNA samples were analyzed as described by Sambrooke et al in Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989) in 0.7% agarose gels in TAE.

DNA and protein analysis

The DNA sequence was analyzed with DNA strider 1.2. The SwissProt database (release Jun. 29, 1994) was searched for homology to all three LlaII amino acid sequences of SEQ ID NO:1.

Isolation of pSRQ700

For many years, Lactococcus lactis subsp. cremoris DCH-4 has performed very well during the industrial buttermilk and sour cream production. One reason for continued good performance is the natural resistance of DCH-4 to lactococcal bacteriophages. One objective of this invention was to identify and transfer the DNA responsible for the phage resistance of DCH-4. The total plasmid DNA of DCH-4 was isolated and co-electroporated with the vector pSA3 into the phage sensitive-plasmid free L. lactis LM0230. The latter strain was selected because it can propagate phages from two species, 936 and c2. The DNA ratio of DCH-4:pSA3 used for electroporation was about 10:1. Em-resistant colonies were tested for phage resistance by spot assay (10³ -10⁴ pfu of .O slashed.p2/spot). A few phage resistant colonies were obtained, analyzed, and found to contain pSA3 and a 7.8 kb low copy plasmid which was named pSRQ700 (FIG. 1). The transformant containing pSRQ700 was named L. lactis SMQ-17 (NRRL-B-21337). Plasmid pSRQ700 was also electroporated into L. lactis UL8 which can propagate phages from the P335 species. The transformant was named L. lactis SMQ-87.

Effectiveness of pSRQ700 on lactococcal phage species

L. lactis SMQ-17 and SMQ-87 were tested for phage resistance against a total of 9 phages belonging to 3 species (3 phages/species). Phages p2, sk1 and jj50 were selected as representatives of the 936 species (Table 1). The lactococcal phage species c2 was represented by the phages c2, ml3 and eb1. These six phages were individually tested on SMQ-17 and their EOPs are presented in Table 3.

                  TABLE 3     ______________________________________     Comparison between the efficiency of plaquing     of lactococcal phages on L. lactis SMQ-17 and     the number of Mbol sites in the phage genome.                 EOP on Number of                 SMQ-17 Mbol sites*     ______________________________________     936 species     .o slashed.p2 1.7 ± 10.sup.-6                            11     .o slashed.sk1                   2.5 ± 10.sup.-6                            9     .o slashed.jj50                   2.0 ± 10.sup.-6                            10     c2 species     .o slashed.c2 1.0 ± 10.sup.-4                            3     .o slashed.ml3                   6.1 ± 10.sup.-3                            2     .o slashed.eb1                   5.5 ± 10.sup.-3                            2     P335 species     .o slashed.ul36                   2.7 ± 10.sup.-7                            13     .o slashed.Q30                   5.2 ± 10.sup.-6                            12     .o slashed.Q33                   1.3 ± 10.sup.-7                            15     ______________________________________      *Only number of fragments >0.5 kb were determined.

The new emerging P335 species was represented by the phages ul36, Q30 and Q33. They were tested separately on SMQ-87 and their EOPs are also presented in Table 3. All three 936 phages had similar EOPs in the range of 10⁻⁶. More variability was observed with the c2 species where EOPs ranged from 10⁻³ to 10⁻⁴. The P335 phages were the most affected by pSRQ700 since EOPs of 10⁻⁷ were observed (Table 3). Identical results were obtained when phage resistance was tested at 21, 30 and 38° C. (data not shown). These results indicated that the phage resistance mechanism encoded on pSRQ700 is temperature insensitive.

Identification of the phage resistance mechanism on pSRQ700

Phages capable of overcoming the defense mechanism encoded on pSRQ700 were isolated. These phages had EOPs of 1.0 on L. lactis SMQ-17. When these resistant (modified) phages were propagated back on their original host, they became sensitive (restricted) to pSRQ700 at the same previous level (data not shown). This temporary host specific immunity, demonstrates the presence of a classical R/M system encoded on pSRQ700. The R/M system was named LlaII.

Isolation of the restriction endonuclease

The non-specific nucleases were removed after ion exchange chromatographies performed on phosphocellulose (Whatman P11) and dimethylaminoethyl cellulose (Whatman DE5) using a salt gradient in PME (10 mM NaH₂ PO₄ pH 7.4, 0.1 mM EDTA and 10 mM β-mercaptoethanol) buffer. DNAs from the well-characterized lactococcal phage ul36 (Moineau, S., et al., Can. J. Microbiol. 38:875-882 (1992: Moineau, S., et al., Appl. Environ. Microbiol. 59:197-202 (1993); and Moineau, S., et al., Appl. Environ. Microbiol. 60:;1832-1841 (1994)) was digested with LlaII. The digestions were conducted overnight at 37° C. since the R/M encoded on pSRQ700 is temperature-insensitive (up to 38° C.). Defined DNA fragments were identified on agarose gels (data not shown). No attempts were made to determine the number of activity units in the collected fractions nor the percentage of recovery from the crude supernatant. Unexpectedly, the restriction patterns obtained corresponded to MboI restriction patterns. Attempts to cut pSRQ700 with MboI were unsuccessful. It was concluded that the R/M system present on pSRQ700 was similar to the MboI system which recognized the sequence 5'-GATC-3' and cleaved it before the guanine.

Mapping of pSRQ700

Single, double and triple digestions were performed with endonucleases to obtain a map of pSRQ700. The results are presented in FIG. 2. The following endonucleases did not cut pSRQ700: ApaI, AvaI, AvaII, BalI, BamHI, HpaI, MboI, PstI, PvuII, SalI, SmaI, SphI, XbaI, XhoI.

Localization of the LlaII system on pSRQ700

The LlaII R/M system was entirely cloned into E. coli using the E. coli-L. lactis shuttle vector pSA3 (FIG. 3). Since appropriate unique restriction sites were present on PSA3 and PSRQ700, total plasmid DNA from L. lactis SMQ-17 was directly used for cloning. Plasmid DNA from SMQ-17 was digested with selected endonucleases, phenol extracted, ethanol precipitated, ligated and the ligation mixture electroporated in E. coli DH5α. This strategy was very effective because expected clones were rapidly obtained. The clones were electroporated into L. lactis LM0230 and phage resistance was determined. The relevant clones are presented in FIG. 3. The entire R/M system of PSRQ700 was localized on a 3-kb NruI-EcoRV fragment. The PSA3 clone containing this 3 kb fragment was named pSRQ706. Similar EOPs were obtained with PSRQ700 and PSRQ706 (FIG. 3). This is due to the similar low copy number of PSA3 and PSRQ700 (FIG. 1).

DNA Sequence Analysis of the LlaII

The 3-kb NruI-EcoRV fragment containing the LlaII genes was sequenced in both directions and found to contain 2,987 bp (FIGS. 4A to 4C; SEQ ID NO:1). This fragment was 65.7% A+T rich, typical of lactococcal genes (Van de Guchte, M., et al., FEMS Microbiol. Rev. 88:73-92 (1992)). Three overlapping open reading frames (orfs) were found and the genes were named LlaIIA, LlaIIB and LlaIIC. In reference to FIGS. 4A to 4C and SEQ ID NO:1, the gene LlaIIA was localized from position 97 to position 948 and coded for a protein of 284 amino acids with an estimated weight of 33,031 Da. The gene LlaIIB was localized from position 941 to position 1747 and coded for a protein of 269 amino acids with an estimated weight of 30,904 Da. The gene LlaIIC was localized from position 1740 to position 2651 and coded for a protein of 304 amino acids with an estimated weight of 34,720 Da. Phage p2 EOP of 1.0 on L. lactis harboring pSRQ702 or pSRQ703 suggested that LlaIIC coded for the endonuclease (FIG. 3). No putative ribosome binding site (RBS) was found for LlaIIA and LlaIIB. A putative RBS (GGAG) was found preceding LlaIIC. Atypical RBS have been identified for the DpnII methylases which are similar to LlaII (FIGS. 5A to 5C). They were not found in the LlaII system. Atypical RBS may be related to translational control of the methylase gene expression (Lacks, S. A., et al., In:Genetics and Molecular Biology of Streptococci, Lactococci and Enterococci, Dunny, G. M., P. P. Cleary and L. L. McKay. (eds) ASM, Washington, D.C. p.71-76 (1991)). All three genes appear to be under the control of the same promoter. However, no definite consensus E. coil-10 and -35 promoter sequences could be identified. Because EOPs were the same in PSRQ700, pSRQ701 and PSRQ703 (FIG. 3), it is believed that the promoter was present in the 3.0-kb fragment. The putative promoter sequences upstream of LlaIIA is of interest. A putative -35 region was localized at position 27, followed by a 18 bp spacer, and a putative -10 region at position 51 (FIGS. 4A to 4C). A search for palindromic sequences identified two perfect inverted repeats of 19 bp, typical of a strong rho-independent terminator, at the very end of LlaIIC (FIGS. 4A to 4C). Interestingly, the stop codon of LlaIIC was within the beginning of the stemloop structure.

Protein analysis

Homology searches showed that the deduced protein coded by LlaIIA was 75.4% identical to DpnII methylase (Mannarelli, B. M., et al., Proc. Natl. Acad. Sci. 82:4468-4472 (1985)), 41.5% identical MboI methylase (Ueno, T., et al., Nucleic Acids Res. 10:2309-2313 (1993)) and 30.1% to the Dam methylase of E. coli (Brooks, J. E., et al., Nucleic Acids Res. 11:837-851 (1983)). It was concluded that LlaIIA codes for a methylase and was named M.LlaIIA. All three methylases (M.DpnII, M.MboA and Dam) homologous to LlaIIA are N-6 adenine methyltransferase (m⁶ A-MTases). The most conserved amino acid sequence motifs among the m⁶ A-Mtases are F-G-G (motif I) and DPPY (motif II). Their organization in the protein allowed the division of the m⁶ A-Mtases in three subclasses (α, β and γ). In the m⁶ A-Mtase subclass a, the motif I is found close to the N-terminal followed by a variable region of 100-200 aa and the motif II close to the C-terminal. The reverse situation is found in the subclass β, where the motif II appears before the motif I. M.LlaIIA has all the characteristics of a m⁶ A-Mtase subclass α:F-G-G motif, a 146 aa variable region and a DPPY motif (FIG. 5). The F-G-G motif probably contained the S-adenosylmethionine binding site and DPPY might be involved in the methylation of exocyclic amino acids (Klimasauskas, S., et al., Nucleic Acids Res. 17:9823-9832 (1989)).

The deduced protein coded by LlaIIB was found to be 88.9% identical to the second methylase of DpnII (Cerritelli, S., et al., Proc. Natl. Acad. Sci. USA, 86:9223-9227 (1989)), 50.2% identical to the second methylase of MboI (Ueno, T., et al., Nucleic Acids Res. 10:2309-2313 (1993)) and 43.6% identical to the HinfI methylase (Chandrasegaran, S., et al., Gene 70:387-392 (1988)). It was concluded that LlaIIB also codes for a methylase and was named M.LlaIIB. All three methylases (M.DpnA, M.MboC and HinfI) homologous to LlaIIB are m⁶ A-Mtases but subclass β. M.LlaIIB has all the subclass β characteristics: a DPPY motif, a 175 aa variable region and a F-G-G motif. Interestingly, FIGS. 5A to 5C also show the amino acid comparison between two sets of four m⁶ A-Mtases isolated from two Gram-positive and two Gramnegative bacteria. This enzyme methylates the same 5'-GATC-3' sequence. Despite the various origins, about 20% and 28% of the amino acids are respectively conserved in the four α and β methylases studied. Interestingly, almost all tryptophan residues are conserved in the methylases studied (FIGS. 5A to 5C).

The deduced protein coded by LlaIIC was 34% and 31% identical to MboI (Ueno, T., et al., Nucleic Acids Res. 10:2309-2313 (1993)) and DpnII (de la Campa, A. G., et al., J. Biol. chem. 263:14696-14702 (1987)) endonucleases, respectively. These results confirmed that LlaIIC coded for an endonuclease and was named R.LlaII. Conserved aa motifs were observed among the three isoschizomers but their functionality is unknown.

It was thus found that Lactococcus lactis subsp cremoris DCH-4 harbors a 7.8-kb low copy plasmid (PSRQ700) coding for a temperature-insensitive R/M system similar to DpnII (Lacks, S. A., et al., In: Genetics and Molecular biology of Streptococci, Lactococci and Enterococci. Dunny, G. M., P. P. Cleary and L. L. McKay. (eds) ASM, Washington, D.C. p-71-76 (1991)) and MboI (Ueno, T., et al., Nucleic Acids Res. 10:2309-2313 (1993)). These systems recognize the non-methylated DNA sequence 5'-GATC-3' where the endonuclease cleaved before the guanine (Lacks, S. A., et al., In: Genetics and Molecular biology of Streptococci, Lactococci and Enterococci. Dunny, G. M., P. P. Cleary and L. L. McKay. (eds) ASM, Washington, D.C. p-71-76 (1991); and (Ueno, T., et al., Nucleic Acids Res. 10:2309-2313 (1993)). The plasmid PSRQ700 is probably one reason for the strong phage resistance shown by DCH-4 over the years. Any phage containing the non-methylated GATC sequence in its genome will be restricted when infecting a L. lactis strain containing PSRQ700.

Members of the three most common lactococcal phage species were strongly restricted by PSRQ700 as shown by their reduced EOPs (Table 3). The small isometric-headed phages of the P335 and 936 species were particularly affected by PSRQ700. This is due in part to their larger genomes. The average genome size for the P335, 936 and c2 phages used in this study was 31.8, 29.7 and 20.2-kb, respectively. However, the most important factor was the number of LlaII sites in the phage genome. Three LlaII sites in the prolate .O slashed.c2 genome were enough to restrict its EOP by 4 logs on L. lactis SMQ-17 (Table 3). Two LlaII sites in the .O slashed.m13 and .O slashed.eb1 genomes were still enough to reduce the EOP by 3 logs. These data are in agreement with the single hit kinetic of R/M system and shows that restriction at one site is enough to prevent phage proliferation (Wilson, G. G., et al., Annu. Rev. Genet. 25:585-627 (1991)). For the small isometric phages which had more LlaII sites in their genome, the presence of 9 to 12 sites gave a 6 log reduction in EOP, whereas 13 to 15 sites were needed for a 7 log reduction. As reported previously, the EOP decreases logarithmically as the number of sites in the phage genome increases (Wilson, G. G., et al., Annu. Rev. Genet. 25:585-627 (1991)).

Thus, phage resistance conferred by PSRQ700 was substantial against members of the 3-lactococcal phage species tested.

Close gene linkage is a feature of all R/M system and accordingly LlaII genes are adjacent (Wilson, G. G., Nucleic Acids Res. 19:2539-2566 (1991); and Wilson, G. G., et al. Annu. Rev. Genet. 25:585-627 (1991)). The LlaII system is highly related to DpnII (Lacks, S. A., et al., In:Genetics and Molecular Biology of Streptococci, Lactococci and Enterococci. Dunny, G. M., P. P. Cleary and L. L. McKay. (eds) ASM, Washington, D. C. p. 71-76 (1991)). They share the same genetic structure: two methylases followed by an endonuclease (de la Campa, A. G., et al., J. Mol. Biol. 196:457-469 (1987)). There is also gene overlapping in both systems. The most striking similarity is their methylases (Cerritelli, S., et al., Proc. Natl. Acad. Sci. USA. 86:9223-9227); and Mannarelli, B. M., et al., Proc. Natl. Acad. Sci. 82:4468-4472 (1985)). Amino acids comparison showed 75% identity between M.LlaIIA and M.DpnII and 88% between M.LlaIIB and M.DpnA (FIG. 5).

Despite the strong homology between LlaII and DpnII methylases, the endonucleases are still divergent. Only 31% of the amino acids are identical. In fact, the endonuclease of LlaII is more homologous to MboI than to DpnII. One might suggest that the methylase had a common ancestor whereas endonucleases evolved independently (Bickle, T. A., et al., Microbiol. Rev. 57:434-450 (1993); (Wilson, G. G., Nucleic Acids Res. 19:2539-2566 (1991); and Wilson, G. G., et al. Annu. Rev. Genet. 25:585-627 (1991)). Many type II R/M system appear to have formed partnerships with miscellaneous genes that were initially separated. They became linked due to a persistent selective advantage (Bickle, T. A., et al., Microbiol. Rev. 57:434-450 (1993); (Wilson, G. G., Nucleic Acids Res. 19:2539-2566 (1991); and Wilson, G. G., et al. Annu. Rev. Genet. 25:585-627 (1991)).

Finally, from a culture manufacturer standpoint, the introduction of the natural low copy number PSRQ700 into industrial Lactococcus lactis strains can confer strong phage resistance against phages of the 936 species and the newly emerging P335 species. Its effectiveness against c2 species will be variable. The temperature insensitivity nature of LlaII (up to 38° C.) makes this phage resistance mechanism amenable to various types of high-temperature dairy fermentations, especially cheese. The use of PSRQ700 as part of a starter rotation scheme (to avoid the build up of modified phages) can improve the overall phage resistance of starter cultures.

EXAMPLE 2

The native LlaII R/M system from Lactococcus lactis was expressed by and conferred strong phage resistance to various industrial S. thermophilus strains. Resistance was observed against phages isolated from yogurt and Mozzarella wheys.

Bacteria, bacteriophages, and media

The strains used in this study are listed in Table 4. S. thermophilus strains were confirmed by Rapid ID 32 Strep (BioMerieux Vitek, Inc., Hazelwood, Mo.). Streptococcus thermophilus strains were grown at 42° C. in GM17. When needed, antibiotics were added at 5 μg of chloramphenicol per ml. Bacteriophages used in this study are listed in Table 4.

                                      TABLE 4     __________________________________________________________________________     Bacteria and bacteriophages used in this study.     Bacteria     or phage             Relevant characteristics.sup.a                                     Source     __________________________________________________________________________     E.coli     DH5α             Transformation host.    Gibco/BRL     L. lactis     LM0230  Plasmid-free, Lac.sup.-, host for .o slashed.p2.                                     38     SMQ-17  LM0230(pSRQ700).        This Invention     SMQ-151 LM0230(pSRQ707), Cm.sup.r.                                     This Invention     S. thermophilus     SMQ-119 Industrial strain used in yogurt, host for .o slashed.Q1 and .o             slashed.Q3.             This Invention     SMQ-146 SMQ-119(PNZ123), Cm.sup.r.                                     This Invention     SMQ-154 SMQ-119(pSRQ707), Cm.sup.r.                                     This Invention     SMQ-173 Industrial strain used for Mozzarella, host for                                     This Invention     SMQ-174 Industrial strain used for Mozzarella, host for                                     This Invention     SMQ-211 SMQ-173(pSRQ707), Cm.sup.r.                                     This Invention     SMQ-212 SMQ-174(pSRQ707), Cm.sup.r.                                     This Invention     Phages     .o slashed.p2             L. lactis phage, small isometric-head, 936 species.                                     L.L. McKay     .o slashed.Q1             S. thermophilus phage isolated from yogurt.                                     This Invention     .o slashed.Q3             S. thermophilus phage isolated from yogurt.                                     This Invention     .o slashed.Q5             S. thermophilus phage isolated from Mozzarella whey.                                     This Invention     .o slashed.Q6             S. thermophilus phage isolated from Mozzarella whey.                                     This Invention     __________________________________________________________________________      L.L. McKay, University of Minnesota; Cm.sup.r, chloramphenicol resistance      Lac.sup.-, deficient in lactose fermenting ability.

Streptococcal phages were propagated by the method of Jarvis et al (Jarvis, A. W., et al., Intervirology 32:2-9 (1991)). EOP assays on S. thermophilus hosts were performed as follows: strains were grown in GM17 overnight at 37° C., 500 μl of cells and 100 μl of diluted phages were mixed with 2.5 ml of soft agar (GM17 supplemented with 10 mM CaCl₂) and layered onto bottom agar (GM17+CaCl₂). Plates were incubated overnight 42° C. in an anaerobic jar (BBL GasPaK Plus, Beckton Dickinson, Cockeysville, Md.).

DNA isolation and manipulation

Plasmid DNA from S. thermophilus was isolated by using the method of O'Sullivan and Klaenhammer (O'Sullivan, D. J., et al., Appl. Environ. Microbiol. 59:2730-2733 (1993) Phage DNA was isolated as described previously (Moineau, S., et al., Appl. Environ. Microbiol. 60:1832-1841 (1994)).

Electroporation

S. thermophilus cells were electroporated as follows: cells were grown in GM17 until mid-exponential phase, centrifuged, washed twice with SG buffer (0.5M sucrose and 10% glycerol) and put on ice until use. Plasmid DNA (1 μg) was mixed with 40 μl of cells in a chilled Gene Pulser cuvette (0.2 cm). The Gene Pulser apparatus (Bio-Rad Laboratories, Richmond, Calif.) was set at 25 μF and 2.45 kV, and the Pulse Controller at 200 Ω. After electroporation, the S. thermophilus cells were immediately resuspended in the rescue broth used for L. lactis cells (Hill, C., FEMS Microbiol. Rev. 12:87-108 (1993)) and incubated for 2 hours at 42° C. before they were plated on GM17 supplemented with the appropriate antibiotic.

Phage isolation

Phages .O slashed.Q1 and .O slashed.Q3 were recently isolated from yogurt samples whereas .O slashed.Q5 and .O slashed.Q6 were isolated also in our laboratory but from Mozzarella whey samples. Phages .O slashed.Q1 and .O slashed.Q3 were then propagated on S. thermophilus SMQ-119, .O slashed.Q5 on SMQ-173 and .O slashed.Q6 on SMQ-174. The genomic DNAs of these streptococcal phages were compared after digestion with EcoRV and MboI (FIG. 6). All four S. thermophilus phages had different restriction patterns (FIG. 6) and consequently they were different.

Expression of LlaII in Streptococcus thermophilus

To verify if LlaII system could be functional in S. thermophilus, the LlaII genes were cloned into a vector with an origin of replication functional in L. lactis and S. thermophilus. The lactic acid bacteria shuttle vector pNZ123 (2.5 kb) (DeVos, W. M., FEMS Microbiol. Rev. 46:281-295 (1987)) was selected. A 7.0-kb EcoRI fragment from pSRQ700 was cloned into the unique EcoRI site of pNZ123 (FIG. 7). The ligation mixture was electroporated directly into the phage sensitive strain L. lactis LM0230. Cm-resistant transformants were obtained and tested for resistance to .O slashed.p2. A phage-resistant transformant thus obtained was named SMQ-151. The resulting pNZ123 clone containing the 7.0 kb fragment from pSRQ700 was named pSRQ707. This plasmid was electroporated into S. thermophilus SMQ-119 and a Cm^(r) -transformant was named SMQ-154. This clone was tested for resistance against two S. thermophilus phages (.O slashed.Q1 and .O slashed.Q3). Both phages were severely restricted on SMQ-154 since they had EOPs of 10⁻⁸ (Table 5).

                  TABLE 5     ______________________________________     Efficiency of Plaquing of S. thermophilus     phages on various hosts.     Phage/Host     EOP     ______________________________________     .O slashed.Q1/SMQ-119                    1.0     .O slashed.Q1/SMQ-146                    1.0     .O slashed.Q1/SMQ-151                    2.4 × 10.sup.-8     .O slashed.Q3/SMQ-119                    1.0     .O slashed.Q3/SMQ-151                    6.1 × 10.sup.-8     .O slashed.Q5/SMQ-173                    1.0     .O slashed.Q5/SMQ-211                    3.9 × 10.sup.-6     .O slashed.Q6/SMQ-174                    1.0     .O slashed.Q6/SMQ-212                    1.2 × 10.sup.-5     ______________________________________

Plasmid pSRQ707 was also electroporated into S. thermophilus SMQ-173 and SMQ-174 which are commercially used for Mozzarella cheese production. Transformants were obtained for both strains, and named SMQ-211 and SMQ-212, respectively. Both transformants were tested for phage resistance. Phage Q5 had an EOP of 10⁻⁶ on SMQ-211 whereas .O slashed.Q6 and an EOP of 10⁻⁵ on SMQ-212 (Table 5). The phage resistance observed against Mozzarella phages was slightly weaker than with the yogurt phages, but still significant. These results show that the LlaII R/M system is functional in various S. thermophilus strains and can confer strong phage resistance in this lactic acid bacteria. This is the first report of increased phage resistance in S. thermophilus.

Thus, in general the present invention relates to an isolated and purified Streptococcus thermophilus naturally lacking in at least one phage resistance and containing recombinant DNA encoding an endonuclease from a Lactococcus lactis to impart the phage resistance.

Further, it relates to a method for fermenting a dairy product, the improvement which comprises using a dairy culture of Streptococcus thermophilus lacking in at least one phage resistance for the fermentation incorporating recombinant DNA encoding an endonuclease of Lactococcus lactis to impart the phage resistance.

Still further, it relates to a method of imparting phage resistance to a Streptococcus thermophilus which is lacking in at least one phage resistance which comprises incorporating recombinant DNA encoding an endonuclease of Lactococcus lactis into the Streptococcus thermophilus to impart the phage resistance.

The foregoing description is only illustrative of the present invention and the present invention is limited only by the hereinafter appended claims.

    __________________________________________________________________________     #             SEQUENCE LISTING     - (1) GENERAL INFORMATION:     -    (iii) NUMBER OF SEQUENCES:  12     - (2) INFORMATION FOR SEQ ID NO:1:     -      (i) SEQUENCE CHARACTERISTICS:     #pairs    (A) LENGTH: 2987 base               (B) TYPE:  Nucleic A - #cid               (C) STRANDEDNESS: Double               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:     #   50GAGCTT TCTAATGCTT AGTGCTTTAA GATTAGGATA GCACGACTTA     #  100TTTTCC AATGAAATTA ACTAGCAATT CGGGTATAAT ATATTTATGA     #  150ATTACA AAAAAACAAG ATCAACTTAC GTCCGTTTAC TAAATGGACA     #  200GGAAAA GGCAACTACT GCCACACATT CAATACCTAA TGCCAGAAAA     #  250AATCAT TTTTTCGAAC CTTTTATTGG TGGTGGCGCT TTGTTTTTTG     #  300CGCTCC TCAAAAAGCA GTTATTAACG ACTTCAATTC TGAGCTTATA     #  350GTTACC GGCAGATGAA AGATAATCCT GAGCAATTGA TAGAATTGTT     #  400AATCAT CAGCGGGAAA ATTCTAAAGA ATATTATTTA GACTTACGTT     #  450TGATAG AGATGGAAGA ATTGATAAGA TGAGCGAAGT TGAACGTGCT     #  500GAATTA TGTATATGCT ACGTGTTGAT TTTAATGGTT TATATCGTGT     #  550TCGAAA AACCAGTTTA ATGTGCCTTA TGGAAGATAT AAAAATCCTA     #  600AGTTGA TAAAGAATTG ATTGAAAGTA TTTCCGAGTA CTTGAATAAC     #  650CTATTA AGATCATGAG TGGAGATTTT GAAAAAGCCG TTAAAGAAGC     #  700GATGGA GATTTTGTTT ATTTCGACCC TCCATACATT CCACTTTCTG     #  750TAGCGC CTTTACTTCT TATACACACG AAGGCTTTAG CTACGAAGAT     #  800TTAGGC TAAGAGATTG TTTCAAACAG TTAGATTCAA AAGGGGTATT     #  850ATGCTT TCAAATTCTT CAAGCCCTTT AGCGGAGGAA TTATATAAAG     #  900TAACAT CCATAAAATT GAAGCTACTC GAACAAATGG GGCTAAATCA     #  950GTCGTG GAAAAATCAC TGAAATCATC GTAACCAATT ATGGCAATTA     # 1000ATATAA GTATGGAGGT GTTTTAATGA CAAAACCATA CTATGAAAAA     # 1050ACGCAA TTCTCGTTCA CGCAGATTCA TTTAAATTAT TAGAAAAAAT     # 1100CCTGAA AGCATGGACA TGATATTTGC TGACCCTCCT TACTTTTTAA     # 1150TGGAGG AATGTCAAAT TCAGGTGGTC AAATTGTTTC TGTTGATAAA     # 1200ATTGGG ATAAAATTTC TTCATTTGAA GAAAAACATG ACTTTAATAG     # 1250TGGATT AGGTTAGCAA GATTGGTTTT AAAACCCAAC GGAACTATTT     # 1300TTCCGG AAGCCTTCAT AACATATATT CTGTCGGGAT GGCGCTGGAA     # 1350AAGGTT TCAAAATCTT AAATAATATA ACTTGGCAAA AGACAAATCC     # 1400CCTAAT CTATCATGTC GGTACTTCAC CCACTCTACA GAGACAATTT     # 1450GGCAAG AAAGAACGAT AAAAAATCTC GCCATTATTA TAACTATGAA     # 1500TGAAAG AGTTTAATGA CGGGAAACAA ATGAAAGATG TTTGGACAGG     # 1550CTGACA AAAAAATCAG AAAAATGGGC TGGGAAACAT CCAACTCAGA     # 1600AGAGTA TATTTTAGAA CGGATAATCT TAGCTAGTAC AAAGGAAAAT     # 1650ATATTT TAGACCCTTT CGTCGGAAGT GGAACTACTG GTGTAGTAGC     # 1700AGATTG GGGCGTAAAT TTATTGGGAT TGATTCTGAG AAAGAATATC     # 1750AATTGC TAAAAAAAGG CTAAATAAAG GAGCAACATA TGGACTTTAA     # 1800TACATC GGTTTAGAAT CTGACGATAG ATTAAATGCT TTTATGGCAA     # 1850TTCCGT AACTAATAGA ACTCCCGAAT ACTACGTGAA CTGGGAAAAA     # 1900AACGTG AAACACGAAA ATTTGAATTA GAACTAAATA CTTTAAACTA     # 1950ATTGGG AAAGAAGATA TTTATAGTGA AGCACTTGAA CTATTTACCA     # 2000ACCTGA ATTGCTTAAA GCTATTCCTA GTTTGATTGC TAGTAGAGAT     # 2050CTTTAG ATATACTAAA CATTGACGAA AATGATGATA TGAGTTTTGA     # 2100CTTAAC TTTCTTGTTA TCGACGAAAA TTGTATCGCT GATTATGTAG     # 2150TATTAA CCAGGCAGGT TTACTAGATT TTCTACAGAA TAAAGCAAAA     # 2200CTCTGG TAGACTATGT GTATGGTGTT GAAGCAGGGC TTGATAGCAA     # 2250CGAAAA AACCGAAGCG GTACAACCAT GGAGGGGATT TTAGAACGTA     # 2300TTCAAA AATAGCTCAA GAGAAAGGGC TTGAATGGAA GCCACAGGCA     # 2350CTTCTT TTATCAAGTC TCAATGGGAC ATAGAAGTCC CTGTAGATAA     # 2400AAAAGA CGCTTTGATG CAGCAGTTTA CTCTCGTGCG CTCAATAAGG     # 2450GCTCAT AGAAACAAAT TACTACGGCG GTGGAGGAAG TAAACTCAAA     # 2500TTGCTG GAGAATTTAC AGAATTGAGT CAGTTTGTAA AAACATCAAA     # 2550AATGTT GAATTTGTAT GGGTAACAGA CGGCCAAGGG TGGAAATTTT     # 2600CTTACC ACTTGCAGAA GCTTTCGGAC ACATCGATAA CGTTTTCAAT     # 2650CCATGT TGAAAGAAGG TTTCTTATCT GATTTATTCG AAAAAGAAAT     # 2700AAAGAC AGAGAATCTC TGTCTTTTTA AATTTCAATT CCTTCCTTCT     # 2750GCTATA ACTTTCCAAA AAACCTGAAA AACGGTTCTG TTGCAATTGT     # 2800GGGGTC GGAACTTACT ACTATATCAT GAGAAATGAA GATTAAAGTT     # 2850CAAAAA AACAGATTAT TTTAAAATGT AAATCTGTTT TTGTTTGGGC     # 2900TTTATC ACACCAATTC TATGTTCAGA AAATGGTCAT TTTCTGGACA     # 2950TCTTTT GTTATTAAAA CTCTCAAAAT CATTTACATT TATTGTTCAT     #           2987ATTCTAT GTTCATTTAT AGATATC     - (2) INFORMATION FOR SEQ ID NO:2:     -      (i) SEQUENCE CHARACTERISTICS:     #Acids    (A) LENGTH: 284 Amino               (B) TYPE:  Amino Aci - #d               (C) STRANDEDNESS: Single               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:  Peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:     - Met Asn Leu Leu Gln Lys Asn Lys Ile Asn Le - #u Arg Pro Phe Thr     #                 15     - Lys Trp Thr Gly Gly Lys Arg Gln Leu Leu Pr - #o His Ile Gln Tyr     #                30     - Leu Met Pro Glu Lys Tyr Asn His Phe Phe Gl - #u Pro Phe Ile Gly     #                45     - Gly Gly Ala Leu Phe Phe Glu Pro Ala Pro Gl - #n Lys Ala Val Ile     #                60     - Asn Asp Phe Asn Ser Glu Leu Ile Asn Cys Ty - #r Arg Gln Met Lys     #                75     - Asp Asn Pro Glu Gln Leu Ile Glu Leu Leu Th - #r Asn His Gln Arg     #                90     - Glu Asn Ser Lys Glu Tyr Tyr Leu Asp Leu Ar - #g Ser Ser Asp Arg     #                105     - Asp Gly Arg Ile Asp Lys Met Ser Glu Val Gl - #u Arg Ala Ala Arg     #               120     - Ile Met Tyr Met Leu Arg Val Asp Phe Asn Gl - #y Leu Tyr Arg Val     #               135     - Asn Ser Lys Asn Gln Phe Asn Val Pro Tyr Gl - #y Arg Tyr Lys Asn     #               150     - Pro Lys Ile Val Asp Lys Glu Leu Ile Glu Se - #r Ile Ser Glu Tyr     #               165     - Leu Asn Asn Asn Ser Ile Lys Ile Met Ser Gl - #y Asp Phe Glu Lys     #               180     - Ala Val Lys Glu Ala Gln Asp Gly Asp Phe Va - #l Tyr Phe Asp Pro     #               195     - Pro Tyr Ile Pro Leu Ser Glu Thr Ser Ala Ph - #e Thr Ser Tyr Thr     #               210     - His Glu Gly Phe Ser Tyr Glu Asp Gln Val Ar - #g Leu Arg Asp Cys     #               225     - Phe Lys Gln Leu Asp Ser Lys Gly Val Phe Va - #l Met Leu Ser Asn     #               240     - Ser Ser Ser Pro Leu Ala Glu Glu Leu Tyr Ly - #s Asp Phe Asn Ile     #               255     - His Lys Ile Glu Ala Thr Arg Thr Asn Gly Al - #a Lys Ser Ser Ser     #               270     - Arg Gly Lys Ile Thr Glu Ile Ile Val Thr As - #n Tyr Gly Asn     #               280     - (2) INFORMATION FOR SEQ ID NO:3:     -      (i) SEQUENCE CHARACTERISTICS:     #Acids    (A) LENGTH: 269 Amino               (B) TYPE:  Amino Aci - #d               (C) STRANDEDNESS: Single               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:  Peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:     - Met Ala Ile Asn Glu Tyr Lys Tyr Gly Gly Va - #l Leu Met Thr Lys     #                 15     - Pro Tyr Tyr Glu Lys Glu Asn Ala Ile Leu Va - #l His Ala Asp Ser     #                30     - Phe Lys Leu Leu Glu Lys Ile Lys Pro Glu Se - #r Met Asp Met Ile     #                45     - Phe Ala Asp Pro Pro Tyr Phe Leu Ser Asn Gl - #y Gly Met Ser Asn     #                60     - Ser Gly Gly Gln Ile Val Ser Val Asp Lys Gl - #y Asp Trp Asp Lys     #                75     - Ile Ser Ser Phe Glu Glu Lys His Asp Phe As - #n Arg Arg Trp Ile     #                90     - Arg Leu Ala Arg Leu Val Leu Lys Pro Asn Gl - #y Thr Ile Trp Val     #                105     - Ser Gly Ser Leu His Asn Ile Tyr Ser Val Gl - #y Met Ala Leu Glu     #               120     - Gln Glu Gly Phe Lys Ile Leu Asn Asn Ile Th - #r Trp Gln Lys Thr     #               135     - Asn Pro Ala Pro Asn Leu Ser Cys Arg Tyr Ph - #e Thr His Ser Thr     #               150     - Glu Thr Ile Leu Trp Ala Arg Lys Asn Asp Ly - #s Lys Ser Arg His     #               165     - Tyr Tyr Asn Tyr Glu Leu Met Lys Glu Phe As - #n Asp Gly Lys Gln     #               180     - Met Lys Asp Val Trp Thr Gly Ser Leu Thr Ly - #s Lys Ser Glu Lys     #               195     - Trp Ala Gly Lys His Pro Thr Gln Lys Pro Gl - #u Tyr Ile Leu Glu     #               210     - Arg Ile Ile Leu Ala Ser Thr Lys Glu Asn As - #p Tyr Ile Leu Asp     #               225     - Pro Phe Val Gly Ser Gly Thr Thr Gly Val Va - #l Ala Lys Arg Leu     #               240     - Gly Arg Lys Phe Ile Gly Ile Asp Ser Glu Ly - #s Glu Tyr Leu Lys     #               255     - Ile Ala Lys Lys Arg Leu Asn Lys Gly Ala Th - #r Tyr Gly Leu     #               265     - (2) INFORMATION FOR SEQ ID NO:4:     -      (i) SEQUENCE CHARACTERISTICS:     #Acids    (A) LENGTH: 304 Amino               (B) TYPE:  Amino Aci - #d               (C) STRANDEDNESS: Single               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:  Peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4:     - Met Asp Phe Asn Asn Tyr Ile Gly Leu Glu Se - #r Asp Asp Arg Leu     #                 15     - Asn Ala Phe Met Ala Thr Leu Ser Val Thr As - #n Arg Thr Pro Glu     #                30     - Tyr Tyr Val Asn Trp Glu Lys Val Glu Arg Gl - #u Thr Arg Lys Phe     #                45     - Glu Leu Glu Leu Asn Thr Leu Asn Tyr Leu Il - #e Gly Lys Glu Asp     #                60     - Ile Tyr Ser Glu Ala Leu Glu Leu Phe Thr As - #n Gln Pro Glu Leu     #                75     - Leu Lys Ala Ile Pro Ser Leu Ile Ala Ser Ar - #g Asp Thr Ser Leu     #                90     - Asp Ile Leu Asn Ile Asp Glu Asn Asp Asp Me - #t Ser Phe Glu Gln     #                105     - Leu Asn Phe Leu Val Ile Asp Glu Asn Cys Il - #e Ala Asp Tyr Val     #               120     - Asp Phe Ile Asn Gln Ala Gly Leu Leu Asp Ph - #e Leu Gln Asn Lys     #               135     - Ala Lys Arg Ser Leu Val Asp Tyr Val Tyr Gl - #y Val Glu Ala Gly     #               150     - Leu Asp Ser Asn Ala Arg Lys Asn Arg Ser Gl - #y Thr Thr Met Glu     #               165     - Gly Ile Leu Glu Arg Thr Val Ser Lys Ile Al - #a Gln Glu Lys Gly     #               180     - Leu Glu Trp Lys Pro Gln Ala Thr Ala Ser Ph - #e Ile Lys Ser Gln     #               195     - Trp Asp Ile Glu Val Pro Val Asp Lys Ser Ly - #s Arg Arg Phe Asp     #               210     - Ala Ala Val Tyr Ser Arg Ala Leu Asn Lys Va - #l Trp Leu Ile Glu     #               225     - Thr Asn Tyr Tyr Gly Gly Gly Gly Ser Lys Le - #u Lys Ala Val Ala     #               240     - Gly Glu Phe Thr Glu Leu Ser Gln Phe Val Ly - #s Thr Ser Lys Asp     #               255     - Asn Val Glu Phe Val Trp Val Thr Asp Gly Gl - #n Gly Trp Lys Phe     #               270     - Ser Arg Leu Pro Leu Ala Glu Ala Phe Gly Hi - #s Ile Asp Asn Val     #               285     - Phe Asn Leu Thr Met Leu Lys Glu Gly Phe Le - #u Ser Asp Leu Phe     #               300     - Glu Lys Glu Ile     - (2) INFORMATION FOR SEQ ID NO:5:     -      (i) SEQUENCE CHARACTERISTICS:     #Acids    (A) LENGTH: 284 Amino               (B) TYPE:  Amino Aci - #d               (C) STRANDEDNESS: Single               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:  Peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5:     - Met Lys Ile Lys Glu Ile Lys Lys Val Thr Le - #u Gln Pro Phe Thr     #                 15     - Lys Trp Thr Gly Gly Lys Arg Gln Leu Leu Pr - #o Val Ile Arg Glu     #                30     - Leu Ile Pro Lys Thr Tyr Asn Arg Tyr Phe Gl - #u Pro Phe Val Gly     #                45     - Gly Gly Ala Leu Phe Phe Asp Leu Ala Pro Ly - #s Asp Ala Val Ile     #                60     - Asn Asp Phe Asn Ala Glu Leu Ile Asn Cys Ty - #r Gln Gln Ile Lys     #                75     - Asp Asn Pro Gln Glu Leu Ile Glu Ile Leu Ly - #s Val His Gln Glu     #                90     - Tyr Asn Ser Lys Glu Tyr Tyr Leu Asp Leu Ar - #g Ser Ala Asp Arg     #                105     - Asp Glu Arg Ile Asp Met Met Ser Glu Val Gl - #n Arg Ala Ala Arg     #               120     - Ile Leu Tyr Met Leu Arg Val Asn Phe Asn Gl - #y Leu Tyr Arg Val     #               135     - Asn Ser Lys Asn Gln Phe Asn Val Pro Tyr Gl - #y Arg Tyr Lys Asn     #               150     - Pro Lys Ile Val Asp Glu Glu Leu Ile Ser Al - #a Ile Ser Val Tyr     #               165     - Ile Asn Asn Asn Gln Leu Glu Ile Lys Val Gl - #y Asp Phe Glu Lys     #               180     - Ala Ile Val Asp Val Arg Thr Gly Asp Phe Va - #l Tyr Phe Asp Pro     #               195     - Pro Tyr Ile Pro Leu Ser Glu Thr Ser Ala Ph - #e Thr Ser Tyr Thr     #               210     - His Glu Gly Phe Ser Phe Ala Asp Gln Val Ar - #g Leu Arg Asp Ala     #               225     - Phe Lys Arg Leu Ser Asp Thr Gly Ala Tyr Va - #l Met Leu Ser Asn     #               240     - Ser Ser Ser Ala Leu Val Glu Glu Leu Tyr Ly - #s Asp Phe Asn Ile     #               255     - His Tyr Val Glu Ala Thr Arg Thr Asn Gly Al - #a Lys Ser Ser Ser     #               270     - Arg Gly Lys Ile Ser Glu Ile Ile Val Thr As - #n Tyr Glu Lys     #               280     - (2) INFORMATION FOR SEQ ID NO:6:     -      (i) SEQUENCE CHARACTERISTICS:     #Acids    (A) LENGTH: 294 Amino               (B) TYPE:  Amino Aci - #d               (C) STRANDEDNESS: Single               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:  Peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:     - Met Lys Pro Phe Ile Lys Trp Ala Gly Gly Ly - #s Asn Ser Leu Leu     #                 15     - Asp Glu Ile Gln Lys Arg Leu Pro Asp Phe Va - #l His Ser Gln Asp     #                30     - Phe Cys Leu Val Glu Pro Phe Val Gly Gly Gl - #y Ala Val Ser Leu     #                45     - Trp Ala Leu Ser Asp Leu Pro His Leu Lys Gl - #n Leu Val Ile Asn     #                60     - Asp Cys Asn Ala Asp Leu Ile Asn Val Tyr Gl - #n Val Ile Lys Asn     #                75     - Asn Pro Asp Asp Leu Ile Gly Tyr Ile Glu As - #n Leu Gln Ser His     #                90     - Tyr Asp Lys Leu Thr Asp Leu Glu Ser Lys Ly - #s Pro Tyr Phe Tyr     #                105     - His Lys Arg Asp Val Phe Asn Gln Arg Thr Se - #r Asn Asp Ile Glu     #               120     - Gln Ala Gly Leu Phe Ile Phe Leu Asn Lys Se - #r Ala Phe Asn Gly     #               135     - Leu Tyr Arg Val Asn Lys Asn Asn Gln Phe As - #n Val Pro Ile Gly     #               150     - Asn Tyr Lys Lys Pro Thr Phe Val Asp Lys Gl - #u Asn Ile Leu Asn     #               165     - Ile Ser Lys Lys Leu Gln Asn Thr Lys Ile Le - #u Ser Gly Asp Phe     #               180     - Glu Leu Val Leu Ala His Leu Pro Asn Asn Ph - #e Pro Cys Leu Phe     #               195     - Tyr Leu Asp Pro Pro Tyr Arg Pro Ile Ser As - #p Thr Ala Ser Phe     #               210     - Thr Ser Tyr Ser Asp Asn Gly Phe Asp Asp As - #n Glu Gln Lys Arg     #               225     - Leu Ala Asn Phe Cys Lys Lys Ile Asp Lys Le - #u Gly His Tyr Phe     #               240     - Leu Leu Ser Asn Ser Asp Pro Lys Asn Thr As - #n Ser Ser Asp Glu     #               255     - Phe Phe Asp Glu Leu Tyr Gln Asp Phe Lys Il - #e Glu Arg Ile Gln     #               270     - Ala Asn Arg Thr Ile Ser Ala Asn Ser Asn Gl - #y Arg Lys Lys Val     #               285     - Asn Glu Ile Ile Val Ser Asn Gly Val                     290     - (2) INFORMATION FOR SEQ ID NO:7:     -      (i) SEQUENCE CHARACTERISTICS:     #Acids    (A) LENGTH: 278 Amino               (B) TYPE:  Amino Aci - #d               (C) STRANDEDNESS: Single               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:  Peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7:     - Met Lys Lys Asn Arg Ala Phe Leu Lys Trp Al - #a Gly Gly Lys Tyr     #15     - Pro Leu Leu Asp Asp Ile Lys Arg His Leu Pr - #o Lys Gly Glu Cys     #                 30     - Leu Val Glu Pro Phe Val Gly Ala Gly Ser Va - #l Phe Leu Asn Thr     #                 45     - Asp Phe Ser Arg Tyr Ile Leu Ala Asp Ile As - #n Ser Asp Leu Ile     #                 60     - Ser Leu Tyr Asn Ile Val Lys Met Arg Thr As - #p Glu Tyr Val Gln     #                 75     - Ala Ala Arg Glu Leu Phe Val Pro Glu Thr As - #n Cys Ala Glu Val     #                 90     - Tyr Tyr Gln Phe Arg Glu Glu Phe Asn Lys Se - #r Gln Asp Pro Phe     #                105     - Arg Arg Ala Val Leu Phe Leu Tyr Leu Asn Ar - #g Tyr Gly Tyr Asn     #               120     - Gly Leu Cys Arg Tyr Asn Leu Arg Gly Glu Ph - #e Asn Val Pro Phe     #               135     - Gly Arg Tyr Lys Lys Pro Tyr Phe Pro Glu Al - #a Glu Leu Tyr His     #               150     - Phe Ala Glu Lys Ala Gln Asn Ala Phe Phe Ty - #r Cys Glu Ser Tyr     #               165     - Ala Asp Ser Met Ala Arg Ala Asp Asp Ala Se - #r Val Val Tyr Cys     #               180     - Asp Pro Pro Tyr Ala Pro Leu Ser Ala Thr Al - #a Asn Phe Thr Ala     #               195     - Tyr His Thr Asn Ser Phe Thr Leu Glu Gln Gl - #n Ala His Leu Ala     #               210     - Glu Ile Ala Glu Gly Leu Val Glu Arg His Il - #e Pro Val Leu Ile     #               225     - Ser Asn His Asp Thr Met Leu Thr Arg Glu Tr - #p Tyr Gln Arg Ala     #               240     - Lys Leu His Val Val Lys Val Arg Arg Ser Il - #e Ser Ser Asn Gly     #               255     - Gly Thr Arg Lys Lys Val Asp Glu Leu Leu Al - #a Leu Tyr Lys Pro     #               270     - Gly Val Val Ser Pro Ala Lys Lys                     275     - (2) INFORMATION FOR SEQ ID NO:8:     -      (i) SEQUENCE CHARACTERISTICS:     #Acids    (A) LENGTH: 268 Amino               (B) TYPE:  Amino Aci - #d               (C) STRANDEDNESS: Single               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:  Peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8:     - Met Lys Asn Asn Glu Tyr Lys Tyr Gly Gly Va - #l Leu Met Thr Lys     #15     - Pro Tyr Tyr Asn Lys Asn Lys Met Ile Leu Va - #l His Ser Asp Thr     #                 30     - Phe Lys Phe Leu Ser Lys Met Lys Pro Glu Se - #r Met Asp Met Ile     #                 45     - Phe Ala Asp Pro Pro Tyr Phe Leu Ser Asn Gl - #y Gly Ile Ser Asn     #                 60     - Ser Gly Gly Gln Val Val Ser Val Asp Lys Gl - #y Asp Trp Asp Lys     #                 75     - Ile Ser Ser Phe Glu Glu Lys His Glu Phe As - #n Arg Lys Trp Ile     #                 90     - Arg Leu Ala Lys Glu Val Leu Lys Pro Asn Gl - #y Thr Val Trp Ile     #                105     - Ser Gly Ser Leu His Asn Ile Tyr Ser Val Gl - #y Met Ala Leu Glu     #               120     - Gln Glu Gly Phe Lys Ile Leu Asn Asn Ile Th - #r Trp Gln Lys Thr     #               135     - Asn Pro Ala Pro Asn Leu Ser Cys Arg Tyr Ph - #e Thr His Ser Thr     #               150     - Glu Thr Ile Leu Trp Ala Arg Lys Asn Asp Ly - #s Lys Ala Arg His     #               165     - Tyr Tyr Asn Tyr Asp Leu Met Lys Glu Leu As - #n Asp Gly Lys Gln     #               180     - Met Lys Asp Val Trp Thr Gly Ser Leu Thr Ly - #s Lys Val Glu Lys     #               195     - Trp Ala Gly Lys His Pro Thr Gln Lys Pro Gl - #u Tyr Leu Leu Glu     #               210     - Arg Ile Ile Leu Ala Ser Thr Lys Glu Gly As - #p Tyr Ile Leu Asp     #               225     - Pro Phe Val Gly Ser Gly Thr Thr Gly Val Va - #l Ala Lys Arg Leu     #               240     - Gly Arg Arg Phe Ile Gly Ile Asp Ala Glu Ly - #s Glu Tyr Leu Lys     #               255     - Ile Ala Arg Lys Arg Leu Glu Ala Glu Asn Gl - #u Thr Asn     #               265     - (2) INFORMATION FOR SEQ ID NO:9:     -      (i) SEQUENCE CHARACTERISTICS:     #Acids    (A) LENGTH: 273 Amino               (B) TYPE:  Amino Aci - #d               (C) STRANDEDNESS: Single               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:  Peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:9:     - Met Arg Ile Lys Pro Tyr Phe Glu Ser Asp As - #p Lys Asn Phe Asn     #                 15     - Ile Tyr Gln Gly Asn Cys Ile Asp Phe Met Se - #r His Phe Gln Asp     #                30     - Asn Ser Ile Asp Met Ile Phe Ala Asp Pro Pr - #o Tyr Phe Leu Ser     #                45     - Asn Asp Gly Leu Thr Phe Lys Asn Ser Ile Il - #e Gln Ser Val Asn     #                60     - Lys Gly Glu Trp Asp Lys Asn Asp Asn Glu Al - #a Ser Ile Tyr Asn     #                75     - Phe Asn His Glu Trp Ile Ala Gln Ala Arg Gl - #n Leu Leu Lys Asp     #                90     - Asn Gly Thr Ile Trp Ile Ser Gly Thr His Hi - #s Asn Ile Phe Thr     #                105     - Val Gly Gln Val Leu Lys Glu Asn Asn Phe Ly - #s Ile Leu Asn Ile     #               120     - Ile Thr Trp Glu Lys Pro Asn Pro Pro Pro As - #n Phe Ser Cys Arg     #               135     - Tyr Phe Thr Tyr Ser Ser Glu Trp Ile Ile Tr - #p Ala Arg Lys His     #               150     - Ser Lys Ile Pro His Tyr Phe Asn Tyr Asp Le - #u Met Lys Lys Leu     #               165     - Asn Gly Asp Lys Gln Gln Lys Asp Ile Trp Ar - #g Leu Pro Ala Val     #               180     - Gly Ser Trp Glu Lys Thr Gln Gly Lys His Pr - #o Thr Gln Lys Pro     #               195     - Leu Gly Leu Leu Ser Arg Ile Ile Leu Ser Se - #r Thr Gln Lys Asp     #               210     - Asp Leu Ile Leu Asp Pro Phe Ser Gly Ser Gl - #y Thr Thr Gly Ile     #               225     - Ala Gly Val Leu Leu Asp Arg Asn Tyr Ile Gl - #y Ile Glu Gln Glu     #               240     - Leu Glu Phe Leu Glu Leu Ser Lys Arg Arg Ty - #r His Glu Ile Thr     #               255     - Pro Val Leu Lys Asn Glu Phe Lys Gln Lys Il - #e Arg Lys Gln Ile     #               270     - Ser Ala Ile     - (2) INFORMATION FOR SEQ ID NO:10:     -      (i) SEQUENCE CHARACTERISTICS:     #Acids    (A) LENGTH: 287 Amino               (B) TYPE:  Amino Aci - #d               (C) STRANDEDNESS: Single               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:  Peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:10:     - Met Met Lys Glu Asn Ile Asn Asp Phe Leu As - #n Thr Ile Leu Lys     #                 15     - Gly Asp Cys Ile Glu Lys Leu Lys Thr Ile Pr - #o Asn Glu Ser Ile     #                30     - Asp Leu Ile Phe Ala Asp Pro Pro Tyr Phe Me - #t Gln Thr Glu Gly     #                45     - Lys Leu Leu Arg Thr Asn Gly Asp Glu Phe Se - #r Gly Val Asp Asp     #                60     - Glu Trp Asp Lys Phe Asn Asp Phe Val Glu Ty - #r Asp Ser Phe Cys     #                75     - Glu Leu Trp Leu Lys Glu Cys Lys Arg Ile Le - #u Lys Ser Thr Gly     #                90     - Ser Ile Trp Val Ile Gly Ser Phe Gln Asn Il - #e Tyr Arg Ile Gly     #                105     - Tyr Ile Met Gln Asn Leu Asp Phe Trp Ile Le - #u Asn Asp Val Ile     #               120     - Trp Asn Lys Thr Asn Pro Val Pro Asn Phe Gl - #y Gly Thr Arg Phe     #               135     - Cys Asn Ala His Glu Thr Met Leu Trp Cys Se - #r Lys Cys Lys Lys     #               150     - Asn Lys Phe Thr Phe Asn Tyr Lys Thr Met Ly - #s His Leu Asn Gln     #               165     - Glu Lys Gln Glu Arg Ser Val Trp Ser Leu Se - #r Leu Cys Thr Gly     #               180     - Lys Glu Arg Ile Lys Asp Glu Glu Gly Lys Ly - #s Ala His Ser Thr     #               195     - Gln Lys Pro Glu Ser Leu Leu Tyr Lys Val Il - #e Leu Ser Ser Ser     #               210     - Lys Pro Asn Asp Val Val Leu Asp Pro Phe Ph - #e Gly Thr Gly Thr     #               225     - Thr Gly Ala Val Ala Lys Ala Leu Gly Arg As - #n Tyr Ile Gly Ile     #               240     - Glu Arg Glu Gln Lys Tyr Ile Asp Val Ala Gl - #u Lys Arg Leu Arg     #               255     - Glu Ile Lys Pro Asn Pro Asn Asp Ile Glu Le - #u Leu Ser Leu Glu     #               270     - Ile Lys Pro Pro Lys Val Pro Met Lys Thr Le - #u Ile Glu Ala Asp     #               285     - Phe Leu     - (2) INFORMATION FOR SEQ ID NO:11:     -      (i) SEQUENCE CHARACTERISTICS:     #Acids    (A) LENGTH: 288 Amino               (B) TYPE:  Amino Aci - #d               (C) STRANDEDNESS: Single               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:  Peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:11:     - Met Lys Gln Thr Arg Asn Phe Asp Glu Trp Le - #u Ser Thr Met Thr     #                 15     - Asp Thr Val Ala Asp Trp Thr Tyr Tyr Thr As - #p Phe Pro Lys Val     #                30     - Tyr Lys Asn Val Ser Ser Ile Lys Val Ala Le - #u Asn Ile Met Asn     #                45     - Ser Leu Ile Gly Ser Lys Asn Ile Gln Glu As - #p Phe Leu Asp Leu     #                60     - Tyr Gln Asn Tyr Pro Glu Ile Leu Lys Val Va - #l Pro Leu Leu Ile     #                75     - Ala Lys Arg Leu Arg Asp Thr Ile Ile Val Ly - #s Asp Pro Ile Lys     #                90     - Asp Phe Tyr Phe Asp Phe Ser Lys Arg Asn Ty - #r Ser Ile Glu Glu     #                105     - Tyr Thr Met Phe Leu Glu Lys Ser Gly Ile Ph - #e Asp Leu Leu Gln     #               120     - Asn His Leu Val Ser Asn Leu Val Asp Tyr Va - #l Thr Gly Val Glu     #               135     - Val Gly Met Asp Thr Asn Gly Arg Lys Asn Ar - #g Thr Gly Asp Ala     #               150     - Met Glu Asn Ile Val Gln Ser Tyr Leu Glu Al - #a Glu Gly Tyr Ile     #               165     - Leu Gly Glu Asn Leu Phe Lys Glu Ile Glu Gl - #n Asn Glu Ile Glu     #               180     - Glu Ile Phe Ser Val Asp Leu Ser Ala Ile Th - #r Asn Asp Gly Asn     #               195     - Thr Val Lys Arg Phe Asp Phe Val Ile Lys As - #n Glu Gln Val Leu     #               210     - Tyr Leu Ile Glu Val Asn Phe Tyr Ser Gly Se - #r Gly Ser Lys Leu     #               225     - Asn Glu Thr Ala Arg Ser Tyr Lys Met Ile Al - #a Glu Glu Thr Lys     #               240     - Ala Ile Pro Asn Val Glu Phe Met Trp Ile Th - #r Asp Gly Gln Gly     #               255     - Trp Tyr Lys Ala Lys Asn Asn Leu Arg Glu Th - #r Phe Asp Ile Leu     #               270     - Pro Phe Leu Tyr Asn Ile Asn Asp Leu Glu Hi - #s Asn Ile Leu Lys     #               285     - Asn Leu Lys     - (2) INFORMATION FOR SEQ ID NO:12:     -      (i) SEQUENCE CHARACTERISTICS:     #Acids    (A) LENGTH: 280 Amino               (B) TYPE:  Amino Aci - #d               (C) STRANDEDNESS: Single               (D) TOPOLOGY:  Linear     -     (ii) MOLECULE TYPE:  Peptide     -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12:     - Met Lys Leu Ala Phe Asp Asp Phe Leu Asn Se - #r Met Ser Glu Thr     #                 15     - Asn Thr Thr Leu Asp Tyr Phe Thr Asp Phe As - #p Lys Val Lys Lys     #                30     - Asn Val Ala Gln Ile Glu Ile His Leu Asn Gl - #n Leu Asn Tyr Leu     #                45     - Leu Gly Lys Asp Asp Leu Lys Gln Ala Val Ty - #r Asp Leu Tyr Ala     #                60     - Glu Cys Pro Asn Ala Phe Ser Ile Leu Glu Il - #e Leu Ile Ala Val     #                75     - Arg Lys Lys Glu Gln Lys Lys Ser Leu Asp Gl - #u Lys Gly Gln Val     #                90     - Val Thr Leu Asn Ser Tyr Phe Gln Ser Ala As - #p Lys Ile Ile Asp     #                105     - Phe Leu Asn Asn Thr Gly Leu Ala Asp Val Ph - #e Arg Asp Lys Asn     #               120     - Ile Lys Asn Leu Val Asp Tyr Val Phe Gly Il - #e Glu Val Gly Leu     #               135     - Asp Thr Asn Ala Arg Lys Asn Arg Gly Gly As - #p Asn Met Ser Lys     #               150     - Ala Val Gln Leu Leu Phe Asp Asn Ala Asp Il - #e Tyr Tyr Lys Lys     #               165     - Glu Val Arg Asn Thr Ile Phe Thr Asp Ile Gl - #u Ser Leu Gly Ala     #               180     - Asp Val Lys Gln Phe Asp Phe Val Ile Lys Th - #r Lys Arg Lys Thr     #               195     - Tyr Val Ile Glu Thr Asn Tyr Tyr Asn Ser Gl - #y Gly Ser Lys Leu     #               210     - Asn Glu Val Ala Arg Ala Tyr Thr Asp Val Al - #a Pro Lys Ile Asn     #               225     - Gln Tyr Ser Gln Tyr Glu Phe Val Trp Ile Th - #r Asp Gly Gln Gly     #               240     - Trp Lys Thr Ala Lys Asn Lys Leu Gln Glu Al - #a Tyr Thr His Ile     #               255     - Pro Ser Val Tyr Asn Leu Tyr Thr Leu His Gl - #y Phe Ile Glu Gln     #               270     - Leu Asn Ser Glu Gly Val Ile Lys Asp Trp     #               280     __________________________________________________________________________ 

We claim:
 1. In a method for fermenting a dairy product, the improvement which comprises using a dairy culture selected from the group consisting of Lactococcus lactis and Streptococcus salivarius subsp. thermophilus containing recombinant DNA encoding an enzyme a member selected from the group consisting of LlaIIA, LlaIIB, LlaIIC and combinations thereof to impart phage resistance, wherein the DNA for the member is contained in strain Lactococcus lactis SMQ-17 deposited as NRRL-B-21337.
 2. The method of claim 1 wherein the DNA is in a vector which was used to transform the culture.
 3. In a method for fermenting a dairy product, the improvement which comprises using a dairy culture of Streptococcus salivarius subsp. thermophilus containing recombinant DNA encoding at least one enzyme of Lactococcus lactis selected from the group consisting of LlaIIA, LlaIIB, LlaIIC, as set forth in SEQ ID NOS. 2, 3 and 4, and combinations thereof to impart phage resistance.
 4. The method of claim 3 wherein the DNA is in a vector which was used to transform the culture.
 5. The method of claim 1 wherein the DNA is selected from the group consisting of ORF1 (positions 97 to 948), ORF2 (positions 941 to 1747), ORF3 (positions 1740 to 2651) of FIG. 4 (SEQ ID NO:1) and combinations thereof.
 6. The method of claim 2 wherein the DNA is selected from the group consisting of ORF1 (positions 97 to 948), ORF2 (positions 941 to 1747), ORF3 (positions 1740 to 2651) of FIG. 4 (SEQ ID NO:1) and combinations thereof.
 7. The method of claim 1 wherein the DNA encodes LlaIIA and the DNA has a nucleotide sequence as set forth in nucleotides 97 to 948 of SEQ ID NO:1.
 8. The method of claim 3 wherein the DNA encodes the enzyme LlaIIA and the DNA has a nucleotide sequence as set forth in nucleotides 97 to 948 of SEQ ID NO.1.
 9. The method of claim 1 wherein the DNA encodes the enzyme LlaIIB and the DNA has a nucleotide sequence as set forth in nucleotides 941 to 1747 of SEQ ID NO.1.
 10. The method of claim 3 wherein the DNA encodes the enzyme LlaIIB and the DNA has a nucleotide sequence as set forth in nucleotides 941 to 1747 of SEQ ID NO.1.
 11. The method of claim 1 wherein the DNA encodes an enzyme LlaIIC and the DNA has a nucleotide sequence as set forth in nucleotides 1740 to 2651 of SEQ ID NO.1.
 12. The method of claim 3 wherein the DNA encodes an enzyme LlaIIC and the DNA has a nucleotide sequence as set forth in nucleotides 1740 to 2651 of SEQ ID NO.1.
 13. The method of any one of claims 1, 5, 7, 9 and 11 wherein the DNA is in a plasmid.
 14. The method of any one of claims 3, 6, 8, 10 or 12 wherein the DNA is in a plasmid. 